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Crystal structure of human purine nucleoside phosphorylase mutant H257D with Imm-H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.974 α = 90 b = 142.974 β = 90 c = 168.55 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2006-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.100 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.592 30 99.3 0.088 0.071 7.1 6.9 20698 20554 67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.592 2.69 94.6 0.625 0.62 1.2 5.3 1945
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RR6 2.592 29.06 20731 20551 1051 99.13 0.207 0.207 0.205 0.2158 0.252 0.2603 RANDOM 62.374
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 25.728 r_dihedral_angle_3_deg 22.196 r_dihedral_angle_1_deg 7.457 r_mcangle_it 3.158 r_scangle_it 2.546 r_angle_refined_deg 2.219 r_mcbond_it 1.878 r_scbond_it 1.661 r_nbtor_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 25.728 r_dihedral_angle_3_deg 22.196 r_dihedral_angle_1_deg 7.457 r_mcangle_it 3.158 r_scangle_it 2.546 r_angle_refined_deg 2.219 r_mcbond_it 1.878 r_scbond_it 1.661 r_nbtor_refined 0.36 r_nbd_refined 0.335 r_symmetry_vdw_refined 0.233 r_xyhbond_nbd_refined 0.215 r_symmetry_hbond_refined 0.192 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling